5YP2 | pdb_00005yp2

Crystal structure of dipeptidyl peptidase IV (DPP IV) with DPP4 inhibitor from Pseudoxanthomonas mexicana WO24

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5YP1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293.15	12% PEG 20000, 100mM MES pH6.5, 20% Glycerol, 1.5mM inhibitor 1c

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.88	α = 90
b = 120.22	β = 90
c = 231.89	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	95	PIXEL	DECTRIS PILATUS 2M		2012-06-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-1A	1.100	Photon Factory	BL-1A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.13	44.05	99.3	0.14	0.154	0.063	0.994	9	5.8		93976

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.13	2.17	90.8		0.876	0.972	0.413	0.61	2	5.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5YP1	2.13	40	89236	4652	99.23	0.18028	0.17787	0.19	0.22627	0.23	RANDOM	32.091

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.76			-0.81		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.277
r_dihedral_angle_4_deg	19.46
r_dihedral_angle_3_deg	15.063
r_dihedral_angle_1_deg	7.321
r_long_range_B_refined	6.256
r_long_range_B_other	6.232
r_scangle_other	4.744
r_mcangle_it	3.592
r_mcangle_other	3.592
r_scbond_it	3.148
r_scbond_other	3.148
r_mcbond_it	2.517
r_mcbond_other	2.516
r_angle_refined_deg	1.864
r_angle_other_deg	1.052
r_chiral_restr	0.104
r_bond_refined_d	0.017
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11320
Nucleic Acid Atoms
Solvent Atoms	700
Heterogen Atoms	58

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
XSCALE	data scaling
MOLREP	phasing